Despite her Spanish roots, the ambitious Luisa guided her husband's policies during the Portuguese revolution against Habsburg Spain of 1640. She is considered the main influence behind his acceptance of the Portuguese throne when the Revolution seemed to tend to the Portuguese side. It is said that being warned of the dangers of becoming queen of a country that was to face Spain's might she pronounced the famous words:

Rather queen for a day (in some versions an hour) than a duchess all my life.

When she was made aware of a failed attempt to murder the King in 1641, she is said to have been one of the members of the Corte, which supported the execution of nobles like the Duke of Caminha.

In 1656, she was named Regent of the Kingdom after her husband's death and during the minority of her son Afonso VI. She continued to occupy the post even after Afonso became an adult because her son was mentally unstable. She was the target of a failed conspiracy headed by Luís de Vasconcelos e Sousa, Count of Castelo Melhor.

She defended the principles of freedom and independence of Portugal and controlled the government with a strong hand, fearing her son was incapable.

Luisa was mainly responsible for the diplomatic success of the new alliance with England. Her daughter Catherine married Charles II of England. She is also credited with the organization of the armies that in the following years would completely ensure Portuguese independence through the victories in the Portuguese Restoration War.